Defence Force chief Lieutenant-General Tim Keating is stepping down from the role, but says Operation Burnham had no influence in his decision.
He won't seek reappointment at the end of his term on June 30.
Keating revealed his decision in an email to staff today, saying it had been his absolute privilege to have served in the role since January 2014.
Keating's announcement comes during close scrutiny over the Defence Force's admission last month that photos in Nicky Hager and Jon Stephenson's book Hit & Run were accurate - reversing the Defence Force's initial claim that it never operated in the photographed areas in the Afghanistan operation.
"One thing I wish to place on record is that my departure had nothing to do with the recent spurious publicity about Operation Burnham – a 2010 NZSAS operation in Afghanistan.